Sample Resequencing Stats
Note: The mutation counts shown below represent unfiltered mutation sets.
| ALE, Flask, Isolate |
Predicted Mutations |
Mean Coverage |
Total Reads |
Percent Mapped |
Mapped Reads |
Average Read Length |
|
A1 F17 I0 R2
|
276 |
45.3 |
3729697 |
93.0% |
3468618 |
60.6 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
W3110S.gb |
3,194,164 |
T→C |
80.9% |
T416A (ACG→GCG) |
rfaE ← |
fused heptose 7‑phosphate kinase and heptose 1‑phosphate adenyltransferase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 3,194,164 | 0 | T | C | 80.9%
| 103.9
/ 18.8
| 47 | T416A (ACG→GCG) | rfaE | fused heptose 7‑phosphate kinase and heptose 1‑phosphate adenyltransferase |
| Reads supporting (aligned to +/- strand): ref base T (2/7); new base C (19/19); total (21/26) |
| Fisher's exact test for biased strand distribution p-value = 1.60e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.77e-01 |
GGTTTATAGTCGCCGCCTTTCACCAGCAGATCTGGCAAGATCCCGGCGATCAAGCGCTGCGGCGTGTCCTCTTCAAACGACACTACCCAGTCGACCGCTTCCAGTGCGCCCAGCACAATCAT > W3110S.gb/3194100‑3194221
|
ggTTTATAGTCGCCGCCTTTCACCAGCAGATCTGGCAAGATCCCGGCGATCAAGCGCTGCGGCGCGTc < 1:2723772/68‑1 (MQ=255)
tataGTCGCCGCCTTTCACCAGCAGATCTGGCAAGATCCCGGCGATCAAGCGCTGCGGCGCGTCctct > 1:3112549/1‑68 (MQ=255)
gccgccTTTCACCAGCAGATCTGGCAAGATCCCGGCGATCAAGCGCTGCGGCGTGTCCTCTTCAAACGa < 1:3633953/69‑1 (MQ=255)
ccTTTCACCAGCAGATCTGGCAAGATCCCGGCGATCAAGCGCTGCGGCGTGTCCTCTTCAAACGacacc < 1:888795/69‑2 (MQ=255)
ccTTTCACCAGCAGATCTGGCAAGATCCCGGCGATCAAGCGCTGCGGCGTGTCCTCTTCAAACGACACt < 1:837648/69‑1 (MQ=255)
tttCACCAGCAGATCTGGCAAGATCCCGGCGATCAAGCGCTGCGGCGCGTCCTCTTCAAACGACACTa > 1:1653658/1‑68 (MQ=255)
tttCACCAGCAGATCTGGCAAGATCCCGGCGATCAAGCGCTGCGGCGCGTACTCTTCAAACGACACTa > 1:1000906/1‑68 (MQ=255)
tCACCAGCAGATCTGGCAAGATCCCGGCGATCAAGCGCTGCGGCGCGTCct < 1:4049/51‑1 (MQ=255)
tCACCAGCAGATCTGGCAAGATCCCGGCGATCAAGCGCTGCGGCGCGTCct < 1:913581/51‑1 (MQ=255)
tCACCAGCAGATCTGGCAAGATCCCGGCGATCAAGCGCTGCGGCGCGTCCTCTTCa > 1:355219/1‑56 (MQ=255)
tCACCAGCAGATCTGGCAAGATCCCGGCGATCAAGCGCTGCGGCGCGTCCTCTTCa > 1:3274336/1‑56 (MQ=255)
tCACCAGCAGATCTGGCAAGATCCCGGCGATCAAGCGCTGCGGCGCGTCCTCTTCa > 1:2628232/1‑56 (MQ=255)
cagcagATCTGGCAAGATCCCGGCGATCAAGCGCTGCGGCGCGTCCTCTTCAAACGACACTACCCAGTc < 1:2591391/69‑1 (MQ=255)
cagcagATCTGGCAAGATCCCGGCGATCAAGCGCTGCGGCGCGTCCTCTTCAAACGACACTACCCAGTc < 1:2801354/69‑1 (MQ=255)
gcagATCTGGCAAGATCCCGGCGATCAAGCGCTGCGGCGCGTCCTCTTCa > 1:561319/1‑50 (MQ=255)
gcagATCTGGCAAGATCCCGGCGATCAAGCGCTGCGGCGCGTCCTCTTCa > 1:1580486/1‑50 (MQ=255)
gcagATCTGGCAAGATCCCGGCGATCAAGCGCTGCGGCGCGTCCTCTTCa > 1:1805260/1‑50 (MQ=255)
gcagATCTGGCAAGATCCCGGCGATCAAGCGCTGCGGCGCGTCCTCTTCa < 1:2866231/50‑1 (MQ=255)
gcagATCTGGCAAGATCCCGGCGATCAAGCGCTGCCGCGCGTCCTCTTCa < 1:3038363/50‑1 (MQ=39)
gATCTGGCAAGATCCCGGCGATCAAGCGCTGCGGCGTGTCCTCTTCAAACGACACTACCCAGTCGACCg > 1:3715880/1‑69 (MQ=255)
gATCTGGCAAGATCCCGGCGATCAAGCGCTGCGGCGTGTCCTCTTCAAACGACACTACCCAGTCGACCg > 1:2342726/1‑69 (MQ=255)
gATCTGGCAAGATCCCGGCGATCAAGCGCTGCGGCGCGTCCTCTTCa < 1:1241668/47‑1 (MQ=255)
cTGGCAAGATCCCGGGGATCAAGCGCTGCGGCGCGTCCTCTTCAAACGACACTACCCAGTCGACCGCt > 1:2247476/1‑68 (MQ=255)
cTGGCAAGATCCCGGCGATCAAGCGCTGCGGCGCGTCCTCTTCa > 1:96025/1‑44 (MQ=255)
cTGGCAAGATCCCGGCGATCAAGCGCTGCGGCGCGTCCTCTTCa > 1:1335600/1‑44 (MQ=255)
cTGGCAAGATCCCGGCGATCAAGCGCTGCGGCGCGTCCTCTTCa > 1:1646079/1‑44 (MQ=255)
cTGGCAAGATCCCGGCGATCAAGCGCTGCGGCGCGTCCTCTTCAAACGACACTACCCAGTCGACCg < 1:1644809/66‑1 (MQ=255)
cTGGCAAGATCCCGGCGATCAAGCGCTGCGGCGCGTCCTCTTCAAACGACACTACCCAGTCGACCg < 1:1042001/66‑1 (MQ=255)
cTGGCAAGATCCCGGCGATCAAGCGCTGCGGCGCGTCCTCTTCAAACGACACTACCCAGTCGACCGCt > 1:1049610/1‑68 (MQ=255)
cTGGCAAGATCCCGGCGATCAAGCGCTGCGGCGCGTCCTCTTCAAACGACACTACCCAGTCGACCGCt > 1:1299236/1‑68 (MQ=255)
cTGGCAAGATCCCGGCGATCAAGCGCTGCGGCGCGTCCTCTTCAAACGACACTACCCAGTCGACCGCt > 1:230799/1‑68 (MQ=255)
cTGGCAAGATCCCGGCGATCAAGCGCTGCGGCGCGTCCTCTTCAAACGACACTACCCAGTCGACCGCt > 1:2649633/1‑68 (MQ=255)
cTGGCAAGATCCCGGCGATCAAGCGCTGCGGCGCGTCCTCTTCAAACGACACTACCCAGTCGACCGCt > 1:1481825/1‑68 (MQ=255)
aGATCCCGGCTATCAAGCGCTGCGGCGCGTCCTCTTCAAACGACACTACCCAGTCGACCGCTTc < 1:3452927/64‑1 (MQ=255)
aGATCCCGGCGATCAAGCGCTGCGGCGCGTCCTCTTCAAACGACACTACCCAGTCGACCGCTTc < 1:2649919/64‑1 (MQ=255)
tCCCGGCGATCAAGCGCTGCGGCGCGTCCTCTTCAAACGACACTACCCAGTCGACCGCTTc < 1:1206924/61‑1 (MQ=255)
cccGGCGATCAAGCGCTGCGGCGTGTCCTCTTCAAACGACACTACCCAGTCGACCGCTTcc < 1:3562410/61‑1 (MQ=255)
cccGGCGATCAAGCGCTGCGGCGTGTCCTCTTCAAACGACACTACCCAGTCGACCGCTTcc < 1:2925809/61‑1 (MQ=255)
ggCGATCAAGCGCTGCGGCGTGTCCTCTTCAAACGACACTACCCAGTCGACCGCTTCCAGTGCGCCCAg < 1:634155/69‑1 (MQ=255)
cAAGGGCTGCGGCGCGTCCTCTTCAAACGACACTACCCAGTCGACCGCTTCCAGTGCGCCCAGCACAAt < 1:1249539/69‑1 (MQ=255)
cAAGCGCTGCGGCGCGTCCTCTTCAAACGACACTACCCAGTCGACCGCTTCCAGTGCGCCCAGCACAAt > 1:404445/1‑69 (MQ=255)
cAAGCGCTGCGGCGCGTCCTCTTCAAACGACACTACCCAGTCGACCGCTTCCAGTGCGCCCAGCACAAt < 1:1087153/69‑1 (MQ=255)
aaGCGCTGCGGCGTGTCCTCTTCAAACGACACTACCCAGTCGACCGCTTCCAGTGCGCCCAGCACAAt < 1:3085373/68‑1 (MQ=255)
gcgcTGCGGCGCGTCCTCTTCAAACGACACTACCCAGTCGACCGCTTCCAGTGCGCCCAGCACAATCAt < 1:2760283/69‑1 (MQ=255)
gcgcTGCGGCGCGTCCTCTTCAAACGACACTACCCAGTCGACCGCTTCCAGTGCGCCCAGCACAATCAt < 1:3496753/69‑1 (MQ=255)
gcgcTGCGGCGCGTCCTCTTCAAACGACACTACCCAGTCGACCGCTTCCAGTGCGCCCAGCACAATCAt < 1:237548/69‑1 (MQ=255)
gcgcTGCGGCGCGTCCTCTTCAAACGACACTACCCAGTCGACCGCTTCCAGTGCGCCCAGCACAATCAt < 1:2935865/69‑1 (MQ=255)
|
GGTTTATAGTCGCCGCCTTTCACCAGCAGATCTGGCAAGATCCCGGCGATCAAGCGCTGCGGCGTGTCCTCTTCAAACGACACTACCCAGTCGACCGCTTCCAGTGCGCCCAGCACAATCAT > W3110S.gb/3194100‑3194221
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
